PXD014357

PXD014357 is an original dataset announced via ProteomeXchange.

Title	Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates
Description	Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a thousand ORFs in exponentially-growing wildtype yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and tRNA adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output compared to other transcripts with equally high ribosome densities.
HostingRepository	PRIDE
AnnounceDate	2019-09-11
AnnouncementXML	Submission_2019-09-11_10:09:26.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD014357
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Schmidt
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	Label:13C(6)15N(2); Label:13C(6)15N(4); Oxidation; Acetyl; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-24 04:16:54	ID requested
⏵ 1	2019-09-11 10:09:27	announced

Riba A, Di Nanni N, Mittal N, Arhn, é E, Schmidt A, Zavolan M, Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates. Proc Natl Acad Sci U S A, 116(30):15023-15032(2019) [pubmed]

submitter keyword: translation, yeast, protein charge, TASEP, ribosomal proteins

Alexander Schmidt
contact affiliation	Biozentrum, University of Basel, CH-4056 Basel, Switzerland
contact email	alex.schmidt@unibas.ch
lab head
Alexander Schmidt
contact affiliation	Proteomics Core Facility
contact email	alex.schmidt@unibas.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD014357
     1. Label: PRIDE project
     2. Name: Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates